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Items: 19

1.

MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets.

Naegle KM, Welsch RE, Yaffe MB, White FM, Lauffenburger DA.

PLoS Comput Biol. 2011 Jul;7(7):e1002119. doi: 10.1371/journal.pcbi.1002119. Epub 2011 Jul 21.

2.

Global quantification of mammalian gene expression control.

Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M.

Nature. 2011 May 19;473(7347):337-42. doi: 10.1038/nature10098. Erratum in: Nature. 2013 Mar 7;495(7439):126-7.

PMID:
21593866
3.

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data.

Lan A, Smoly IY, Rapaport G, Lindquist S, Fraenkel E, Yeger-Lotem E.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W424-9. doi: 10.1093/nar/gkr359. Epub 2011 May 16.

4.

Identifying causal genes and dysregulated pathways in complex diseases.

Kim YA, Wuchty S, Przytycka TM.

PLoS Comput Biol. 2011 Mar;7(3):e1001095. doi: 10.1371/journal.pcbi.1001095. Epub 2011 Mar 3.

5.

Finding undetected protein associations in cell signaling by belief propagation.

Bailly-Bechet M, Borgs C, Braunstein A, Chayes J, Dagkessamanskaia A, François JM, Zecchina R.

Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):882-7. doi: 10.1073/pnas.1004751108. Epub 2010 Dec 27.

6.

An integrated approach to uncover drivers of cancer.

Akavia UD, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, Causton HC, Pochanard P, Mozes E, Garraway LA, Pe'er D.

Cell. 2010 Dec 10;143(6):1005-17. doi: 10.1016/j.cell.2010.11.013. Epub 2010 Dec 2.

7.

The challenges of integrating multi-omic data sets.

Palsson B, Zengler K.

Nat Chem Biol. 2010 Nov;6(11):787-9. No abstract available.

PMID:
20976870
8.

Cytoscape Web: an interactive web-based network browser.

Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD.

Bioinformatics. 2010 Sep 15;26(18):2347-8. doi: 10.1093/bioinformatics/btq430. Epub 2010 Jul 23.

9.

Associating genes and protein complexes with disease via network propagation.

Vanunu O, Magger O, Ruppin E, Shlomi T, Sharan R.

PLoS Comput Biol. 2010 Jan 15;6(1):e1000641. doi: 10.1371/journal.pcbi.1000641.

10.

Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks.

Huang SS, Fraenkel E.

Sci Signal. 2009 Jul 28;2(81):ra40. doi: 10.1126/scisignal.2000350.

11.

Information flow analysis of interactome networks.

Missiuro PV, Liu K, Zou L, Ross BC, Zhao G, Liu JS, Ge H.

PLoS Comput Biol. 2009 Apr;5(4):e1000350. doi: 10.1371/journal.pcbi.1000350. Epub 2009 Apr 10.

12.

Integrating siRNA and protein-protein interaction data to identify an expanded insulin signaling network.

Tu Z, Argmann C, Wong KK, Mitnaul LJ, Edwards S, Sach IC, Zhu J, Schadt EE.

Genome Res. 2009 Jun;19(6):1057-67. doi: 10.1101/gr.087890.108. Epub 2009 Mar 4.

13.

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity.

Yeger-Lotem E, Riva L, Su LJ, Gitler AD, Cashikar AG, King OD, Auluck PK, Geddie ML, Valastyan JS, Karger DR, Lindquist S, Fraenkel E.

Nat Genet. 2009 Mar;41(3):316-23. doi: 10.1038/ng.337. Epub 2009 Feb 22.

14.

STRING 8--a global view on proteins and their functional interactions in 630 organisms.

Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C.

Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6. doi: 10.1093/nar/gkn760. Epub 2008 Oct 21.

15.

Identifying functional modules in protein-protein interaction networks: an integrated exact approach.

Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Müller T.

Bioinformatics. 2008 Jul 1;24(13):i223-31. doi: 10.1093/bioinformatics/btn161.

16.

eQED: an efficient method for interpreting eQTL associations using protein networks.

Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T.

Mol Syst Biol. 2008;4:162. doi: 10.1038/msb.2008.4. Epub 2008 Mar 4.

17.

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments.

Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R.

Bioinformatics. 2007 Jul 1;23(13):i359-66.

PMID:
17646318
18.

Physical network models.

Yeang CH, Ideker T, Jaakkola T.

J Comput Biol. 2004;11(2-3):243-62.

PMID:
15285891
19.

Inferring cellular networks using probabilistic graphical models.

Friedman N.

Science. 2004 Feb 6;303(5659):799-805. Review.

PMID:
14764868

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